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ARS Home » Southeast Area » Charleston, South Carolina » Vegetable Research » Research » Publications at this Location » Publication #325480
Research Project: Sustainable Approaches for Pest Management in Vegetable Crops

Location: Vegetable Research

Title: Genome sequencing of the sugarcane aphid for microsatellite development and endosymbiont detection

Author
item Wadl, Phillip
item Harris-Shultz, Karen
item Wang, Xinwang
item Ni, Xinzhi

Submitted to: International Congress of Entomology
Publication Type: Abstract Only
Publication Acceptance Date: 5/16/2017
Publication Date: 8/22/2017
Citation: Wadl, P.A., Harris-Shultz, K.R., Wang, X., Ni, X. 2017. Genome sequencing of the sugarcane aphid for microsatellite development and endosymbiont detection [abstract]. XXV International Congress of Entomology. doi:10.1603./ICE.2016.108446.

Interpretive Summary: N/A

Technical Abstract: Introduction: The sugarcane aphid (Melanaphis sacchari) is one of the most important insect pests on grain sorghum in 17 southern U.S. states in 2015. The aphid infestations are causing crop loss or yield loss depending on the timing of the aphid infestations occurred at either pre- or post-anthesis. Few markers are available for studying genetic diversity of sugarcane aphid. Our goal was to develop a large set of microsatellites for M. sacchari from genome sequencing and identify the associated symbionts. Methods: We sequenced genomic DNA from a single sugarcane aphid using the Ion Torrent PGM™. After quality trimming, a total of 1.44 Gb was generated. Because almost all aphid species have associations with microbes inside their eukaryotic cells we filtered the M. sacchari reads with the reference genome sequences of the known symbiont genomes associated with aphid species. Results/Conclusions: After filtering of the symbiont reads, 78.4% of the reads were M. sacchari. The largest percent of the symbiont reads were Verticillium spp. (6.0%) and Buchera aphidicola (5.6%). Contigs = 10X coverage (n = 2,424) from M. sacchari were screened for microsatellites and 1,455 were identified and 1,179 primer pairs were designed. Microsatellites were only detected in B. aphidicola, Hamiltonella defensa, Regiella insecticola, and Serratia symbiotica and 34 primer pairs were designed. We are currently utilizing the microsatellites to characterize the sugarcane aphid populations collected from multiple locations in the US and expect these markers to be valuable for monitoring genetic diversity of this new pest on sorghum.